package se.cbb.scripts;

import java.io.BufferedReader;
import java.io.FileReader;
import java.util.ArrayList;

import se.cbb.misc.Sequence;
import se.cbb.misc.SequenceFileWriter;
import se.cbb.misc.SimpleFileIO;

public class VMCMCScriptGenerator {

	public static void main(String[] args) {
		try {
			String path = "/Users/rhali/Desktop/";
			String str;
//			int index = 1;
			
			BufferedReader bufferedreader = new BufferedReader(new FileReader(path + "FileNames.txt"));
			while ((str = bufferedreader.readLine()) != null) {
				SequenceFileWriter.writeAndAppendLine(path, "ParallelAnalysis.sh", "java -Xmx3600m -Xms3200m -jar VMCMC-1.0.0.jar ./Informed/MCMC/InformedGeneTree" + str + ".mcmc ./Uninformed/MCMC/GeneTree" + str + ".mcmc -o " + str + ".par -b1 0 -b2 0");
//				index++;
			}
			
			bufferedreader.close();
		} catch (Exception e) {
			System.out.println("Error : " + e.getMessage());
		}


	}

}
